MICROBIAL PHYSIOLOGY AND FERMENTATION TECHNOLOGY 2020

Day 1 Monday, 20 January

Themes: Thermodynamics, balances and q-rates
Coordinator: Han de Winde

08.45-09.00 Registration

09.00-09.15 Outline of the course

Han de Winde

09.15-10.15 Basic energetics of microbial metabolism Chapter 1

Robbert Kleerebezem

10.15-10.30 Break

10.30-11.30 Balances Chapter 2a

Sef Heijnen

11.30-11.45 Break

11.45-12.15 q-rates Chapter 2b

Sef Heijnen

12.15-12.20 Photographer

12.20-13.15 Lunch @Bar ‘t Lab (TNW-Zuid)

13.15-15.15 Parallel sessions:

Exercises on energetics of microbial metabolism Exercise Ch1
Robbert Kleerebezem

Exercises on balances and q-rates Exercise Ch2

Sef Heijnen

15.15-15.30 Break

15.30-17.30 Continuation of the parallel sessions

17.30-17.40 Evaluations

17.45-20.00 Welcome drinks and buffet @Bar ‘t Lab (TNW-Zuid)

MICROBIAL PHYSIOLOGY AND FERMENTATION TECHNOLOGY 2020

Day 2 Tuesday, 21 January

Themes: Kinetics and stoichiometry of growth, product formation, process design and
membranes transport
Coordinator: Sef Heijnen

09.00-10.00 Batch, fed batch and continuous cultivation Chapter 3

Aljoscha Wahl

10.00-10.15 Break

10.15-11.15 Black box model: kinetics / parameterization Chapter 4a/b

Sef Heijnen

11.15-11.30 Break

11.30-12.30 Black box model: stoichiometry Chapter 4c

Sef Heijnen

12.30-13.30 Lunch @Bar ‘t Lab (TNW-Zuid)

13.30-14.15 Introduction to bioprocess design (batch, continuous) Chapter 4d

Sef Heijnen

14.15-14.30 Break

14.30-16.00 Exercises on bioprocess reactions in design Exercise Ch4

Sef Heijnen

16.00-16.15 Break

16.15-17.30 Continuation of the exercises

17.30-17.45 Break

17.45-18.30 Transport over biological membranes: mechanisms and

thermodynamics Chapter 5
Walter van Gulik

18.30-18.40 Evaluations
MICROBIAL PHYSIOLOGY AND FERMENTATION TECHNOLOGY 2020

Day 3 Wednesday, 22 January

Themes: Regulation of metabolism by environmental parameters, fermentation design and
data analysis
Coordinator: Han de Winde

09.00-09.45 Primary metabolism and its regulation Chapter 6

Pascale Daran-Lapujade

09.45-10.00 Break

10.00-10.45 Microbial growth with mixtures of carbon substrates Chapter 7

Han de Winde

10.45-11.00 Break

11.00-12.00 Physiological aspects of high cell density fermentation Chapter 8

Han de Winde

12.00-13.00 Lunch @Bar ‘t Lab (TNW-Zuid)

13.00-13.45 Fed batch fermentation and transport phenomena Chapter 9

- the fermentor
- O2 / CO2 in biological processes
- design of fed-batch fermentation processes
Sef Heijnen

13.45-14.00 Break

14.00-14.30 Continuation

14.30-15.30 Exercises on data analysis of fermentation processes Exercise Ch9

15.30-15.45 Break

15.45-17.00 Continuation exercises

17.00-18.00 Optional: Lab techniques tour department of Biotechnology

followed by drink
MICROBIAL PHYSIOLOGY AND FERMENTATION TECHNOLOGY 2020

Day 4 Thursday, 23 January

Themes: Metabolic networks: stoichiometry, Flash energy and Fed batch demo
Coordinator: Sef Heijnen

09.00-10.00 Metabolic network analysis: Chapter 10

- energy conversion pathways
- from product pathway reaction to network product reaction
- the network biomass reaction
Sef Heijnen

10.00-10.15 Break

10.15-12.30 Exercises: Metabolic pathways stoichiometry Exercise Ch10

12.30-13.30 Lunch @Bar ‘t Lab (TNW-Zuid)

13.30-14.00 Fed batch demo: Stoichiometric network calculation Fed Batch 1

Sef Heijnen

14.00-14.15 Fed batch demo: Fed batch fermentation Fed Batch 2

Sef Heijnen

14.15-14.30 Break

14.30-15.15 Fed batch demo: Design calculation Fed Batch 3

Rob Kerste

15.15-16.00 Fed batch demo: Measurements why and how Fed Batch 4
Rob Kerste

16.00-16.45 Bioenergetics of microbial growth and the cost of adaptation,

Part I Chapter 11
Joost Teixeira de Mattos

16.45-17.00 Break

17.00-17.45 Bioenergetics of microbial growth and the cost of adaptation,

Part II
Joost Teixeira de Mattos

17.45-17.55 Evaluations

18.00-20.00 Buffet @Bar ‘t Lab (TNW-Zuid)

MICROBIAL PHYSIOLOGY AND FERMENTATION TECHNOLOGY 2020

Day 5 Friday, 24 January

Themes: Metabolic networks: stoichiometry, fluxes and high-cell density fed batch
Coordinator: Aljoscha Wahl

09.00-10.00 Metabolic flux balancing: theory and applications Chapter 12

Aljoscha Wahl

10.00-10.15 Break

10.15-12.45 Computer exercises on metabolic network analysis Exercise Ch12

Aljoscha Wahl a.o.

12.45-13.45 Lunch @Bar ‘t Lab (TNW-Zuid)

13.45-14.45 Metabolic studies in the industrial contexts Chapter 13

Ralf Takors

14.45-15.30 Exercises on high-cell density fed batch cultivation Exercise Ch14

Walter van Gulik / Aljoscha Wahl

15.30-15.45 Break

15.45-18.00 Exercises continued

18.00-18.10 Evaluations

18.15-20.00 Social drink @Bar ‘t Lab (TNW-Zuid)

MICROBIAL PHYSIOLOGY AND FERMENTATION TECHNOLOGY 2020

Day 6 Monday, 27 January

Theme: Case study: Ethanol from syngas
Coordinator: Henk Noorman

09.00-09.30 Rate based design of biosystems Chapter 15

Sef Heijnen

09.30-10.00 Case study: Ethanol from syngas Exercise Ch15

General introduction and background Task 1
Henk Noorman / Sef Heijnen

10.00-10.15 Break

10.15-12.15 Calculations Task 1

12.15-12.45 Presentations by each team: results Task 1

Henk Noorman / Sef Heijnen

12.45-14.00 Lunch @Bar ‘t Lab (TNW-Zuid)

13.25-13.55 (optional) Visit fermentation lab (max. 10 persons)

Dirk Geerts / Rob Kerste

14.00-14.30 Background Task 2 Exercise Ch15

Henk Noorman / Sef Heijnen

14.30-16.15 Calculations Task 2

16.15-16.30 Break

16.30-17.00 Presentations by each team: results Task 2

17.00-17.15 Break

17.15-18.15 Gas Fermentation: a path to low carbon fuel and chemical Chapter 16
production with impact
Bjorn Heijstra

18.15-18.25 Evaluations
MICROBIAL PHYSIOLOGY AND FERMENTATION TECHNOLOGY 2020

Day 7 Tuesday, 28 January

Themes: Regulation and control of metabolic fluxes, rapid sampling
Coordinator: Walter van Gulik

09.00-10.00 Multi-scale modelling of process dynamics in large-scale

bioreactors Chapter 17
Matthias Reuss

10.00-10.15 Break

10.15-11.00 Multi-level regulation of metabolic fluxes, transcripts versus fluxes Chapter 18

Pascale Daran-Lapujade

11.00-12.15 Analysis of in vivo kinetics: rapid sampling and metabolite

analysis Chapter 19
Walter van Gulik

12.15-13.15 Lunch

13.15-15.00 Fed batch demo: Balance calculations on batch phase data Fed Batch 5
Sef Heijnen / Dirk Geerts / Rob Kerste / Walter van Gulik

15.00-15.15 Break

15.15-16.00 Through Van Leeuwenhoek’s eyes Chapter 20

Lesley Robertson

16.00-17.30 Van Leeuwenhoek and Delft: A microbiological pilgrimage

(social / cultural event)
Guide: Lesley Robertson

18.00-20.30 Drinks + Small dinner @De Gist

MICROBIAL PHYSIOLOGY AND FERMENTATION TECHNOLOGY 2020

Day 8 Wednesday, 29 January

Theme: Metabolic and community engineering
Coordinator: Han de Winde

09.00-10.15 Metabolic engineering strategies for reducing costs Chapter 21

Sef Heijnen

10.15-10.30 Break

10.30-12.30 Exercises on metabolic engineering strategies for reducing costs Exercise Ch21
Sef Heijnen

12.30-13.30 Lunch @Bar ‘t Lab (TNW-Zuid)

12.55-13.25 (optional) Visit fermentation lab (max. 10 persons)

Dirk Geerts / Rob Kerste

13.30-14.30 From System Biology to Metabolic Engineering and Industrial Process

Development using Clostridium acetobutylicum as a
Platform Strain Chapter 22
Philippe Soucaille

14.30-15.30 Monascus ruber as cell factory for lactic acid production at low pH Chapter 23
Ruud Weusthuis

15.30-15.45 Break

15.45-16.45 Zero growth physiology – from biotechnology to brains Chapter 24

Mark Bisschops

16.45-17.00 Break

17.00-18.00 Microbial community engineering for production of chemicals and Chapter 25

bioenergy
Robbert Kleerebezem

18.00-18.10 Evaluations
MICROBIAL PHYSIOLOGY AND FERMENTATION TECHNOLOGY 2020

Day 9 Thursday, 30 January

Theme: Heterogeneity of microbial populations
Coordinator: Han de Winde

09.00-10.00 Single cell studies of micro-organisms / Microfluidics Chapter 26

Sander Tans

10.00-10.15 Break

10.15-11.15 Spatio-temporal single-cell analysis in picoliter reactors Chapter 27

Dietrich Kohlheyer

11.15-11.30 Break

11.30-12.30 The limits to growth: the challenge to dissipate energy Chapter 28

Matthias Heinemann

12.30-13.30 Lunch @Bar ‘t Lab (TNW-Zuid)

13.30-14.30 Transcription factor-based biosensors for strain development Chapter 29

Jan Marienhagen

14.30-15.30 Fed batch demo: Balance calculations on the fed phase data Fed Batch 6
and evaluation
Sef Heijnen / Dirk Geerts / Rob Kerste / Walter van Gulik

15.30-15.45 Break

15.45-17.00 Continuation and conclusion of fed batch demo

17.00-18.00 Optional: Practical labtour regarding Chemostat

Rob Kerste / Dirk Geerts

18.00-18.10 Evaluations

19.00-22.30 Course diner – Restaurant van der Dussen (Bagijnhof 118, Delft)
MICROBIAL PHYSIOLOGY AND FERMENTATION TECHNOLOGY 2020

Day 10 Friday, 31 January

Theme: Capita Selecta
Coordinator: Sef Heijnen

09.30-10.30 Microbial protein production in an industrial context Chapter 30

Cees Sagt

10.30-10.45 Break

10.45-11.45 High-throughput strain construction and phenotype testing Chapter 31

Stefan de Kok

11.45-13.15 Lunch @Sport&Cultuur (Mekelweg 8-10, Delft)

13.15-14.15 Latest advancements in high-resolution

microbial mass spectrometry Chapter 32
Martin Pabst

14.15-15.00 The Origin of Life and Metabolism Chapter 33

John Sutherland

15.00-15.25 Evaluation and certification

Sef Heijnen

15.25-16.25 Optional: Practical labtour regarding Chemostat

Rob Kerste / Dirk Geerts

15.25-18.00 Farewell drink @Bar ‘t Lab (TNW-Zuid)